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Merged
labkey-martyp merged 4 commits into from
Sep 11, 2026
Merged

Add project, protocol and location to the Rearrival form #758

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1b3e983
Add project, protocol and location to the Rearrival form
labkey-martyp Sep 9, 2026
00e5bdd
Add a Selenium test for the Rearrival form
labkey-martyp Sep 9, 2026
12ec10a
Give draft rearrivals an interim status and drop the no-op cache call
labkey-martyp Sep 9, 2026
4d8d055
Query demographics in the EHR folder, not the project
labkey-martyp Sep 10, 2026
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72 changes: 43 additions & 29 deletions nirc_ehr/resources/queries/study/arrival.js
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Original file line number Diff line number Diff line change
Expand Up @@ -24,41 +24,21 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even

helper.registerArrival(row.Id, row.date);

//Insert or update demographic and birth records
if (!row.rearrival && !helper.isETL() && !helper.isGeneratedByServer() && !helper.isValidateOnly()) {

// this allows demographic records in qcstates other than completed
var extraDemographicsFieldMappings = {
'taskid': row.taskid,
'qcstate': helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId()
}

// null (not undefined) required for call to java trigger helper
row.dam = row['Id/demographics/dam'] || null;
row.sire = row['Id/demographics/sire'] || null;
row.species = row['Id/demographics/species'] || null;
row.birth = row['Id/demographics/birth'] || null;
row.gender = row['Id/demographics/gender'] || null;
row.geographic_origin = row['Id/demographics/geographic_origin'] || null;
row.source = row.sourceFacility || null;
// Project, protocol and housing records are created for rearrivals too: the animal's departure closed the previous ones.
if (!helper.isETL() && !helper.isGeneratedByServer() && !helper.isValidateOnly()) {

if (row.QCStateLabel) {
row.qcstate = helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId();
}

if (row.birth) {
var birthInfo = {
// A rearrival reuses the existing demographics record, so its status is written directly; drafts get the same interim status an arrival draft does.
// The update refreshes the server-side animal cache, so the records opened below validate against this status rather than the departure's.
if (row.rearrival && row.Id && row.QCStateLabel) {
row.calculated_status = (row.QCStateLabel.toUpperCase() === 'IN PROGRESS' || row.QCStateLabel.toUpperCase() === 'REVIEW REQUIRED') ? 'Alive - In Progress' : 'Alive';
helper.getJavaHelper().updateDemographicsRecord([{
Id: row.Id,
date: row.birth,
qcstate: row.qcstate,
taskid: row.taskid,
performedby: row.performedby
}

var birthErrors = triggerHelper.saveBirthRecord(row.Id, birthInfo);
if (birthErrors){
EHR.Server.Utils.addError(scriptErrors, 'birth', birthErrors, 'ERROR');
}
calculated_status: row.calculated_status
}]);
}

if (row.Id && row.date) {
Expand Down Expand Up @@ -100,6 +80,40 @@ EHR.Server.TriggerManager.registerHandlerForQuery(EHR.Server.TriggerManager.Even
EHR.Server.Utils.addError(scriptErrors, 'Id', housingErrors, 'ERROR');
}
}
}

//Insert or update demographic and birth records
if (!row.rearrival && !helper.isETL() && !helper.isGeneratedByServer() && !helper.isValidateOnly()) {

// this allows demographic records in qcstates other than completed
var extraDemographicsFieldMappings = {
'taskid': row.taskid,
'qcstate': helper.getJavaHelper().getQCStateForLabel(row.QCStateLabel).getRowId()
}

// null (not undefined) required for call to java trigger helper
row.dam = row['Id/demographics/dam'] || null;
row.sire = row['Id/demographics/sire'] || null;
row.species = row['Id/demographics/species'] || null;
row.birth = row['Id/demographics/birth'] || null;
row.gender = row['Id/demographics/gender'] || null;
row.geographic_origin = row['Id/demographics/geographic_origin'] || null;
row.source = row.sourceFacility || null;

if (row.birth) {
var birthInfo = {
Id: row.Id,
date: row.birth,
qcstate: row.qcstate,
taskid: row.taskid,
performedby: row.performedby
}

var birthErrors = triggerHelper.saveBirthRecord(row.Id, birthInfo);
if (birthErrors){
EHR.Server.Utils.addError(scriptErrors, 'birth', birthErrors, 'ERROR');
}
}

row.calculated_status = (row.QCStateLabel.toUpperCase() === 'IN PROGRESS' || row.QCStateLabel.toUpperCase() === 'REVIEW REQUIRED') ? 'Alive - In Progress' : 'Alive';

Expand Down
53 changes: 38 additions & 15 deletions nirc_ehr/resources/web/nirc_ehr/model/sources/Rearrival.js
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Original file line number Diff line number Diff line change
Expand Up @@ -30,11 +30,14 @@ EHR.model.DataModelManager.registerMetadata('Rearrival', {
},
},
acquisitionType: {
allowBlank: false,
columnConfig: {
fixed: true,
width: 150
},
allowBlank: true,
hidden: true,
showInGrid: false
},
CITES: {

@ankurjuneja ankurjuneja Sep 10, 2026

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any reason for uppercase?

@labkey-martyp labkey-martyp Sep 11, 2026

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I don't know if it's required necessarily but the column itself is uppercase.

allowBlank: true,
hidden: true,
showInGrid: false
},
arrivalType: {
allowBlank: false,
Expand All @@ -43,20 +46,40 @@ EHR.model.DataModelManager.registerMetadata('Rearrival', {
}
},
'cage': {
allowBlank: true,
hidden: true,
showInGrid: false
allowBlank: false,
columnConfig: {
fixed: true,
width: 200
},
},
project: {
allowBlank: true,
hidden: true,
showInGrid: false
xtype: 'combo',
columnConfig: {
width: 150
},
lookup: {
schemaName: 'ehr',
queryName: 'project',
keyColumn: 'project',
columns: 'project,name',
filterArray: [
LABKEY.Filter.create('isActive', true, LABKEY.Filter.Types.EQUAL),
]
},
allowBlank: false
},
arrivalProtocol: {
allowBlank: true,
hidden: true,
showInGrid: false
allowBlank: false,
columnConfig: {
width: 200
},
lookup: {
schemaName: 'ehr',
queryName: 'activeProtocols',
keyColumn: 'protocol',
columns: 'protocol,title'
},
},
}
}
});
});
68 changes: 68 additions & 0 deletions nirc_ehr/test/src/org.labkey.test/tests.nirc_ehr/NIRC_EHRTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -645,6 +645,74 @@ public void testArrivalForm()
verifyOrchardFileGenerated(arrivedAnimal);
}

@Test
public void testRearrivalForm() throws Exception
{
String rearrivedAnimal = getExpectedAnimalIDCasing("R7373");
LocalDateTime now = LocalDateTime.now();

goToEHRFolder();

log("Seeding an animal that has left the center");
for (String query : List.of("arrival", "departure", "assignment", "protocolAssignment", "housing", "demographics"))
getApiHelper().deleteAllRecords("study", query, new Filter("Id", rearrivedAnimal));

// The departed status is seeded straight onto demographics because a departure does not recalculate
// calculated_status in this module, so inserting one alone would leave the animal alive.
String[] demographicsFields = {"Id", "Species", "Birth", "Gender", "date", "calculated_status", "objectid", "performedby"};
Object[][] demographicsData = {{rearrivedAnimal, "Rhesus", now.minusDays(30).toString(), getMale(), new Date(), "Shipped", UUID.randomUUID().toString(), 1004}};
getApiHelper().doSaveRows(DATA_ADMIN.getEmail(), getApiHelper().prepareInsertCommand("study", "demographics", "lsid", demographicsFields, demographicsData), getExtraContext());

InsertRowsCommand departure = new InsertRowsCommand("study", "departure");
departure.addRow(Map.of("Id", rearrivedAnimal, "date", now.minusDays(2), "destination", "Oregon NPRC", "performedby", 1004));
departure.execute(getApiHelper().getConnection(), getContainerPath());

gotoEnterData();
waitAndClickAndWait(Locator.linkWithText("Rearrivals"));
lockForm();

Ext4GridRef rearrivals = _helper.getExt4GridForFormSection("Rearrivals");
_helper.addRecordToGrid(rearrivals);

log("A rearrival collects project, protocol and location, and does not collect acquisition type or CITES");
Assert.assertTrue("Project should be on the Rearrival form", rearrivals.isColumnPresent("project", true));
Assert.assertTrue("Protocol should be on the Rearrival form", rearrivals.isColumnPresent("arrivalProtocol", true));
Assert.assertTrue("Location should be on the Rearrival form", rearrivals.isColumnPresent("cage", true));
Assert.assertFalse("Acquisition type should not be on the Rearrival form", rearrivals.isColumnPresent("acquisitionType", true));
Assert.assertFalse("CITES should not be on the Rearrival form", rearrivals.isColumnPresent("CITES", true));

rearrivals.setGridCellJS(1, "date", now.minusDays(1).format(DateTimeFormatter.ofPattern(DATE_TIME_FORMAT_STRING)));
rearrivals.setGridCell(1, "arrivalType", "Non-quarantine Arrival");
rearrivals.setGridCell(1, "Id", rearrivedAnimal);
rearrivals.setGridCell(1, "cage", "C1");
rearrivals.setGridCell(1, "project", "640991");
rearrivals.setGridCell(1, "arrivalProtocol", "dummyprotocol");
rearrivals.setGridCell(1, "sourceFacility", "BIOQUAL, Inc.");
submitForm("Submit Final", "Finalize");

goToSchemaBrowser();
DataRegionTable table = viewQueryData("study", "arrival");
table.setFilter("Id", "Equals", rearrivedAnimal);
CustomizeView view = table.openCustomizeGrid();
view.addColumn("cage");
view.addColumn("project");
view.addColumn("arrivalProtocol");
view.applyCustomView();
Assert.assertEquals("Invalid Rearrival record", Arrays.asList("C1"), table.getRowDataAsText(0, "cage"));
Assert.assertEquals("Invalid Rearrival record", Arrays.asList("640991"), table.getRowDataAsText(0, "project"));
Assert.assertEquals("Invalid Rearrival record", Arrays.asList("dummyprotocol"), table.getRowDataAsText(0, "arrivalProtocol"));

log("The rearrival opens the assignment, protocol assignment and housing records that the departure closed");
verifyRowCreated("study", "assignment", rearrivedAnimal, 1);
verifyRowCreated("study", "protocolAssignment", rearrivedAnimal, 1);
verifyRowCreated("study", "housing", rearrivedAnimal, 1);

log("The rearrived animal is alive again");
List<Map<String, Object>> rows = executeSelectRowCommand("study", "demographics", ContainerFilter.Current, "/" + getContainerPath(), List.of(new Filter("Id", rearrivedAnimal))).getRows();
assertEquals("Expected one demographics record for the rearrived animal", 1, rows.size());
assertEquals("Rearrived animal should be alive", "Alive", rows.getFirst().get("calculated_status"));
}

@Test
public void testBirthForm()
{
Expand Down